Error encountered: Exon or junction is zero

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What steps will reproduce the problem?
1. I generated exon coordinate .bed file from Altanalyze.
2. Sort that file using BEDTools.
3. Re-running the Altanalyze

What is the expected output? What do you see instead?
No ouput.

What version of the product are you using? On what operating system?
AltAnalyze v2.0.6 - Windows

Please provide any additional information below.
The .bam file and junctions.bed (from Tophat) is already in the folder. The 
Exon file had been generated from Altanalyze and then used BedTools. Now 
re-running the process arising the problem. Looking forward for your support.

Thank You!

Original issue reported on code.google.com by asma.bio...@gmail.com on 27 May 2012 at 12:27

[GoogleCodeExporter]

The likely problem is that the bed files have chromosomes formatted without 
"chr", so AltAnalyze can't match them to the IDs in is database. This was 
reported recently and fixed for AltAnalyze 2.0.7 which should be released soon. 

If you would like a pre-release instance of this version, please contact me.

Original comment by nsalomo...@gmail.com on 27 May 2012 at 2:46

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Thank You so much for your reply!

Actually both .bed files have the prefix 'chr' in the chromosome number. 
Anyways, I'll try the new version :)

Regards,
Asma

Original comment by asma.bio...@gmail.com on 28 May 2012 at 4:57

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When you say that you generated the exon coordinate .bed file from AltAnalyze 
and then sorted using BEDTools, do you mean you simply used the AltAnalyze .bed 
file as your exon input?

You want to use BEDTools as described here:
http://code.google.com/p/altanalyze/wiki/BEDTools

Where you convert your BAM files to BED files, getting counts for each exon 
from the AltAnalyze supplied BED file template. This will give you a single 
exon.bed file for each and every BAM file which is used as input to AltAnalyze 
as described here:
http://code.google.com/p/altanalyze/wiki/BAMtoBED

Original comment by nsalomo...@gmail.com on 28 May 2012 at 5:21

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Thank you for your quick responses!

Actually I am getting little bit confused now.... :)

Yes, The generated exon coordinate .bed file was used in the BedTools. I am 
only testing one bam file for now. The folder contains .bam file, .bam.bai 
index file and junctions.bed file.

1) Generated the exon coordinate bed file from Altanalyze (Output: 
./BAMtoBED/Hs_sample1_exon.bed). (Successful)

2) Used that Hs_sample1_exon.bed in BEDTools along with accepted_hits.bam to 
convert into bed. (Another .bed file)

3) Try to use the recently generated .bed file in Altanalyze. (Error)

Kindly tell me where am I wrong.... I think it's somewhere in Step-2. Or am I 
going in the right way?

Right now, I am downloading the test sample to test it on Altanalyze. I'll give 
you feedback once it works or not?

Original comment by asma.bio...@gmail.com on 29 May 2012 at 10:45